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RBPmotif specifications

Information


Unique identifier OMICS_03826
Name RBPmotif
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for RBPmotif

RBPmotif citations

 (4)
library_books

RNA Binding Protein Vigilin Collaborates with miRNAs To Regulate Gene Expression for Caenorhabditis elegans Larval Development

2017
PMCID: 5555458
PMID: 28576776
DOI: 10.1534/g3.117.043414

[…] miRNAs and families of miRNAs in regulating the first larval stage of C. elegans development.Although we were not able to determine a high confidence VGLN-1 binding motif using computational methods [RBPMotif ()], the enrichment of specific miRNA target sites among VGLN-1 target mRNAs could suggest that alternative methods of functional selectivity may exist. This enrichment and genetic interactio […]

library_books

Revealing protein–lncRNA interaction

2015
Brief Bioinform
PMCID: 4719072
PMID: 26041786
DOI: 10.1093/bib/bbv031

[…] context of motif discovery at RBP binding sites can be found in []. The already mentioned MEMERIS [], CMfinder [], RNApromo [], StructRED [], the algorithm by Li and collaborators [], RNAcontext and RBPmotif [, ], GraphProt [] and Zagros [] are all tools that use, with different strategies and to different extent, secondary structure information to determine more specific binding motifs.The appli […]

library_books

High throughput characterization of protein–RNA interactions

2014
Brief Funct Genomics
PMCID: 4303715
PMID: 25504152
DOI: 10.1093/bfgp/elu047

[…] condary structure context (e.g. a hairpin loop) and learns the weights for each position from a set of input sequences annotated with relative binding affinity []. RNAcontext is also available on the RBPmotif Web server [].The second approach considers RNA secondary structure explicitly and includes stochastic context-free grammar (SCFG) and graphical approaches. CMfinder [] and RNApromo [] both s […]

library_books

Finding the target sites of RNA binding proteins

2013
PMCID: 4253089
PMID: 24217996
DOI: 10.1002/wrna.1201

[…] binding affinities of the RBP of interest. Each input RNA sequence is scored by using the sequence and structure context parameters. RNAcontext has been applied to in vitro binding-affinity data. The RBPmotif webserver implements RNAcontext. […]

Citations

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RBPmotif institution(s)
Department of Computer Engineering, Antalya International University, Antalya, Turkey

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